The Wicked Ones
by ZoeWalker01
Summary: First he had to get rid of Valentine, then he had to get Angel boy on his side and last but certainly not least he had to meet his little sister. Clonathan
1. Chapter 1

**A/N:**

I'm so sorry for the spelling errors or any errors in general.

He was ready. Finally all his plans would come to function, finally he would have control of everything, all the shadow world would be at his mercy.

Few of his endarkened were waiting for him hidden outside the New York Institute. He managed to create a infernal cup while he's father sent him in long missions and instead of killing the targets his father sent him after he turned them into soulless slaves.

Jonathan geared up. But before he could start he needed to get rid of the old man who, as he expected, was in his study. He knocked loudly on the oak door of Father's study. "Come in". He heard he's father answer with obvious annoyance in his voice. Valentine did not liked to be disturbed. Jonathan closed the door behind him. "What do you want Jonathan"

Jonathan lungged at him with an unnatural speed sending him backwards in his chair. Jonathan grabbed Valentine by the neck of his shirt and slammed his head against the desk before hauling him up and placing a dagger at Valentine's throat. "Jonathan think about what your about to do". The man spoke with some fear in his voice. This emotion didn't pass unnotice by Joanthan. "I have thought of this since the first time you took out that whip". He pressed the dagger lightly against his throat sending a thin line of blood down his neck. "What will you do without me". Valentine continued failing at hiding his fear. "Jonathan please, we can be a family again". The young man was thrilled at hearing him beg for his life. "I already located your mother and your sis-". "Too late for that" Jonathan whispered before slicing his neck. He let Valentine's dead body while a wicked grin crossed his face. Time to meet Angel boy.

Jonathan surveyed the perimeter of the Institute from the outside. "You know your orders" He reminded his group of endarkened and some followers that, chose to follow him and not his father. There was no need to turn them. "Now" He directed, stepping to the side while his crew started to march at the Institute's door.

The Lightwoods heard the hustle coming from the door. And proceed to get their weapons. By the time the made it to the door each one of them where welcomed with a dagger at their neck. "Nice of you to join us" said a mocking voice.


	2. Chapter 2

Chapter 2

Jonathan stepped into the Institute, his endarkened had secured the area already. He wanted this to be over quickly so he could meet Clarissa. He never understood emotions only lust and rage, but thinking about meeting his sister for the first time, getting to know her, having her at his side stirred a complete set of emotions within him. Jonathan had come to terms not to long ago that he would allow himself to feel something more than lust and rage towards her sister, _perhaps love_.

Sure a part of Jonathan's plan consisted of having her on his side. He wanted her in all ways even if some of those ways were frowned upon. Maybe it would take her some time to warm up to _some of the ways_ he wanted her. But he wasn't going to leave New York without her on his side.

The Lightwoods looked around them confused; they had seen Valentine in old photographs. The young man standing in front of them may have had an astounding resemblance to Valentine but certainly it wasn't him. He seemed to look up and down at each one of them like gauging if they were a threat. Apparently not by the look of dismiss on his face.

Jonathan didn't know what to expect from Angel Boy. He would never attmit it out loud but he had been a bit anxious of Angel boy being a better fighter or a better mastermind than himself, but just looking at the emotion and humanity in his eyes told him how mistaken Jonathan was about him. _how pathetic_. Told him how mistaken Jonathan was about him.

Jace tried to get out of the guard's grasp given that he was the only one without a dagger at his throat. He didn't stop to think why. Many thoughts crossed his mind. Why did this guy that showed out of no where looked like a young version of his dead father. "Who are you?!". Jace demanded.

"You don't look to be in the position to be making questions?" The guy said smugly.

Jace looked to one of the shadowhunters that were standing at the door of the Institute, but their eyes seemed soulless which creeped him out even more.

"Take them to cells in the basement". Jonathan said to the endarkened. "Wait for my orders". Jace saw the guards that were holding the daggers to Alec and I Isabelle's neck start to drag them to the halls. Want were they going to do to them? Why wasn't he going with them too? He wanted to protect them.


	3. Chapter 3

"By the look of complete confusion in your face I assume you dont now who I am but look familiar to you".

Jonathan took a step closer. "Do you know who Valentine Morgenstern is?" This was an obvious question but Jonathan wanted to see how he reactions to the name given that he never knew weather he knew about the true identity of the man that raised him. "Of course I know who hr is, the whole shadow world knows who he is".

He didn't know, Jace was oblivious to who he's parents were and even to who had raised him this annoyed Jonathan he would have to explain everything before luring him into joining him. "Do you even know who raised you?". Jonathan asked annoyed.

"Why do I have to answer to you?". Jace challenged him raising his chin.

"Because your real name isn't Wayland". Jonathan was getting bored and wanted this over quickly. "You were raised by Valentine Morgenstern whom is my Father". "That's a lie, my father was Michael Wayland!" He was even mire pathetic than he thought. Jonathan wanted this over now.

"No he wasnt your father, your father was Stephen Herondale, he died and who you thought was Michael Wayland was actually Valentaine Morgenstern".

Jonathan wasnt going to be sensitive about it why the hell would he be but he had to persuade him to come with him by will otherwise keeping him in line would be difficult. By the looks of it the promise of power won't convince him but maybe the promise of knowing the truth would, of course it was going to be the story he decided to tell him.

"Your parents were Stephen and Celine Herondale, they were part of the circle" Jonathan said slowly like if he was talking to a child "Your real father died in a mision and your mother killed herself from grief after that Valentine raised you" He was going to spare the details. "So you must know Valentine has been dead for seven years now". Jace said still not looking gim in the eye. "So what do you want from us". It was time put his cards on the table.

"The clave is currpeted I asume you know this". Jace nodded his head slightly "help me end this corruption". Jonathan could couldn't care less about how corrupted was the clave at the end there would be no clave at all.

"As hell I am going to help you!". Jace shouted. "You walk in here and threten us and then expect us to help you".

"I guess you are just going to make things difficult". Jonathan was done trying to olay nice. He would do things the way he usally did. "Here's the deal you come with me, I will leave your loved ones alone and tell you the truth about your past". "And what if I don't go". Jace said finally lookimg him in the eye. "Then you will have to watch how everything goes down to hell without you being able to do something about it".

"I will go". It wasn't what he said at last wat convinced him it was the promise of knowing what happened to his parents. One of the soldiers that came with the guy came out from Hodge's office his hands were coveres in blood. "Hodge Starkweather is dead, master Jonathan". This so called Jonathan nodded his head in approval. "Why did you have to kill him?". Jace asked facing down to the ground he still was kneeling down and a guard was holding him down. "Hodge Starkwaether was a rat, He was still in an alliance with Valentine and he would have contacted the clave when he found out my father is dead". Jonathan answered. "Valentine died in a mision not long ago". So this dude named Jonathan was the real son of Valentine Morgentern who raised him after his real parents passed away. It was a lot to take in.

Jonathan enjoyed how easy it was lying to him but he still didnt trust him to not run away and tell the clave about his plans or at least what he would confide him with which wasnt much but it still would set back he's plans".

 **A/N: Thanks for reading this and sorry for all the spelling and grammar mistakes I'm gonna try to update sooner I already have the story kind of planned**

 **LOVE Y'ALL**

 **-Zoe**


	4. Chapter 4

Jace got stuck having to follow Jonathan who was a bit ahead of him. He had absolutely no idea what he wanted him for, given that by the looks of it Jonathan didn't like him that much. In fact he seemed to hate him. What did he wanted exactly from him? A few blocks ago he had asked him but he had only responded with "Don't make questions. I'll tell you what you need when the time is right".

"Here we are". Jonathan said, pulling him out of his thoughts.

Jonathan putted the note with Clarissa's address in his pocket. It was an old building. When they got to what was supposed to be her apartment the door was wide open.

Jonathan was worried, Jace could sense this after all if what Jonathan said was true they were both raised by the same man who told them emotions were a weakness. The apartment was a mess, and the smell of blood and sulfur hit his nose. Were they there to hunt a demon?. Jonathan raised a hand in motion for him to stop and took out his blade. Jace did the same. Both of them were in ready for attacking at any time.

"Go check the kitchen, the demon might still be here". Jace only nodded.

Where was she?! a demon had broken into her apartment and now Jonathan feared she might be dead. No, she couldn't be he could feel it she was alive. He heard something there was someone hiding somewhere near the bathroom. Jonathan carefully turned the door knob and opened the door when something crashed against his skull it wasn't strong enough for knocking him off but he staggered back and looked up to see what hit him

an angry little redhead was looking up at him with bright green eyes, ready to hit him again with what seem to be a frying pan. It was he's sister, Clarissa, she was even more beautiful than he had thought.

"You don't look like the thing that attacked me" she said thoughtfully. He was lost looking at her. The fire dancing in her green eyes made him lose himself. "Who are you and what are you doing here." Clary spoke again never backing off like everyone did.

"What?". Jonathan had been lost in his thoughts.

"I said, who are you and what are you doing here". She repeated annoyed.

"I believe I am your brother".

"That's bullshit," Clary frowned. "I never had any siblings".

"Well now you do —"

Clary couldn't hear the rest of it she felt room spinning, what was happening? Was this just a weird dream? And then she felt the darkness drown her.

Dammit, Clary probably had demon venom in her system. He would heal her but first Jonathan had to take care of the demon. He carried Clary to one of the rooms of the apartment and laid her down until it was safe for her.

Jace had been looking for the demon but it had probably escaped by now so his guard was down a bit, when a creature crashed into him trying to cut him or maybe stab him with one of its nails, he quickly maneuvered out of its reach to pull out his seraph blade and whisper and angel's name, Jace was about to charge at the creature when something grabbed him by the back of his shirt. There was another demon looking down at him. It was about to claw its nails to his chest when it burst into flames it had been Jonathan.

 _Pathetic Angel boy,_ Jonathan thought, he left him alone by a few minutes and he almost dies. Jonathan quickly got rid of the other demon meanwhile Jace could get on his feet. It didn't even look like they had been raised by the same man. "Get up, we have to leave". Jonathan commanded. He went to get Clary, he would heal her back at the apartment.

 **A/N:** Heeeeeey thanks a lot for reading this and again, I'm really sorry for all the grammatical and spelling mistakes (I need a beta, please) also I'll probably change the rating to M cuz I want to add some smut later on the story, so how would you feel about that?

LOVE Y'ALL

-Zoe


	5. Chapter 5

"That's bullshit". Clary said annoyed.

She had woken up a few hours ago in a weird place and with a weird mark on her right hand.

The next few hours since her wakening the one who presumed to be her brother had been trying to explain the whole thing about some people called Shadowhunters, and the fact that there were actual vampires, werewolves, and faeries, which apparently weren't as nice as in the movies, also that her mother had lied to her all her life, and—what?

She must have been dreaming, a weird and complex dream. A part of her didn't want to believe what Jonathan was saying, it didn't want to believe that her whole life had been a lie and that the one who had been telling her all this lies had been her mother, who had died two years ago, she still missed her almost every day.

But Clary still wanted to believe in this new world that had just been presented to her, it felt like an explanation she didn't knew how much she wanted.

Jonathan sighted. This was the third time Clarissa said that the shadow world, their world was 'bullshit', he could see in her eyes how she wanted to believe him, though. He had been glad when he found out Jocelyn had died, even though he didn't show it. With Jocelyn dead, he was the only family Clary had left. He kept telling himself how glorious it would be when she finally accepted her place at his side, he was so close, he just had to convince her that they were meant to be together. That she belonged to him and he belonged to her. "I know there's a part of you that believes what I'm saying." He said, choosing his words carefully. "That you want to believe in this new world, trust me, I'll show you everything this world has to offer"

Clary got lost in his eyes, how they seemed to bore into her soul, how his words seemed to mirror her thoughts. Even though she had just met him she felt a pull to him, she wanted to trust him, she knew they were related but why did she felt like there was something else linking her to him. Clary cleared her mind of those thoughts, she must have hit her head pretty hard. She felt compelled to believe in him the part of her that wanted to know this new world was winning. "I trust you."

Jonathan felt some kind of relief —he had never felt relief before.—Clarissa had chosen to trust

him, he was closer than he thought, I knew doubt settled inside him, how was he supposed to show her all the wonders she had been missing living as a mundane and then convince her to be at his side to watch him destroy them?

-XXX-

Clary had been living with Jonathan and Jace for a week know. And it had been the most exciting week of her life. She had seen all kind of thing and had been to all kind of places. Every day they visited a new city, Jonathan and Jace left on the morning for a couple hours and leave her alone but then they would come back and show her any city they would be in. Every day she spent with them made her pull towards Jonathan grow stronger, finding it hard to fight sometimes, it could just be the fact that she was starting to be closer to him, sometimes they would spend nights talking, about everything and anything. He always made sure she had the best of everything but sometimes she felt like he was hiding something.

She had been getting closer to Jace, too but not as much as to Jonathan. He seemed pretty nice and kind but she didn't had the chance to talk to him too often, Jace looked sometimes upset like he didn't wanted to be there with them.

Still, Clary loved being with them, she was currently waiting for them to come back lounging into the living room, enjoying the view of Prague, she thought about getting her sketch pad to draw the scene.

They were on Prague right now, Jonathan had been dragging him from city to city running errands. Jace still couldn't figure out what was his plan, he could try to guess some from the thing they had been getting and doing. The girl that Jonathan had been looking for on his first night with him had turned out to be his sister, she was oblivious to everything they were doing and to most of the shadow world. Jace still couldn't figure out if she was lucky for her lack of knowledge of what her brother was doing or not. Clary wasn't like her brother, she was kind, and caring. Still he couldn't talk much with her, Jonathan had threaten him and his family if he did.

A/N: Heeeeeey guys thank you a lot for reading this story, I'm sorry for all the grammatical and spelling mistakes and for taking too long on update, amd again thank you a lot for the reviews I swear they make my day better.

Love y'all

-Zoe


	6. Chapter 6

Chapter 6

The streets of Prague were silent. There were still a few hours until dawn and Jonathan was dragging Jace on another midnight scavenger. Neither of them told Clary about their midnight searches but it was obvious, at least for Jace, that she was getting suspicious.

They arrived to what seemed like a small antique shop. Jonathan stepped in and Jace followed him. Looking around he realized it was in fact an antique shop but this one had several demonic objects glamorized. Jonathan went to the counter where an odd man was apparently waiting for him. "So I see you decided to go on with that lunatic plan of yours." Said the man putting what seemed like Adams on the counter but immediately stopped talking when he saw Jonathan shoot him a warning glare. Jonathan turned to look at Jace. "Return to the apartment. I'll come back soon." Jace turned to leave but before he could Jonathan added "And don't be an idiot."

Jace knew what he meant by this 'don't be an idiot and run away.' He knew his family would be put at risk if he decided to run away and he didn't want to leave Clary alone with her psychotic brother. He could see the way Jonathan looked at her. It wasn't the normal way a brother looked at his sister.

He felt like slipping. At first, when Jonathan dragged him to his errands which meant killing, torturing and tormenting people he hesitated and only did it when Jonathan directly threatened him with going after his loved ones or doing it himself which assured the victim a much worst faith but now he felt just a pang of remorse afterwards. It was scary how a few weeks with a monster were turning him into one. He needed to get himself and Clary, even though she seemed happy living with her brother, far away from Jonathan.

Jace entered the apartment through the hidden door and turned to see a fully awake Clary sitting on the sofa waiting for him. "Where were you?" She asked. "And where is Jonathan?"

"He'll be back soon." Jace said sitting down on the couch opposite to her . "Why haven't you gone to bed? It is pretty late."

"I couldn't sleep." She lied seeing how Jace tried to avoid her questions. She wasn't stupid she knew they were hiding something and every time Clary tried to ask what was going on the same as tonight would happen, her questions would be avoided or they would change the subject.

"I can't stop thinking abut how my mother could hide all of this from me." She may not appreciate that they were hiding something from her but she still felt Ike she could trust them and didn't thought opening a little bit to Jace would do much harm.

"You know she did it to protect you from Valentine, right?" Jace said looking relieved from the change of subject. "He wasn't a really sane man." Clary saw the expression that Jace had when he talked abut who had been her father, like if he had know him from a long time ago.

"Did you ever met him?" She asked almost in a whisper.

"Met him? Valentine raised me." He answered to looking at the floor.

"I thought you said the Lightwoods had adopted you when your father died?"

"I used to think that was the truth too, Turns out it was Valentine who raised me, pretending to be Michael Wayland and after he realized I was just cutting time from his plans he faked his death. That's how I ended living with the Lightwoods."

"I guess we are all part of 'the screwed up parents' club, huh." Said Clary in a bitter laugh.

"I guess you are right." Said Jace with the same bitter laugh. "Clary you should be more careful around Jonathan." His tone had grown more serious. "Valentine was way more harsh on him than he was on me and I only lived with him for ten years, the angel knows what he did to him and what type of person he is now."

"What are you saying?" Clary said. "I know that he went through a lot living with Valentine but does it make him evil." She took a deep breath and stood up from the couch she was sitting on. She suddenly got the urge to get out of the room so she could think about what Jace had told her. "I think I should go to sleep now, you should too. It is pretty late." Jace seemed to want to add something but decided not to when he saw her expression.

She couldn't sleep last night, her mind kept going back to what Jace had said. It could have gone by as if they had gone into a disagreement and Jace had decided to retaliate trying to make her suspicious of him but she knew that hr brother was up to something not so good. She had seen boys come back from their errands covered in blood, she had heard the whispered threats Jonathan made to Jace. Clary knew that Jace was More like a hostage to Jonathan and the words that Jace had used when he talked about Jonathan just made her confirm her some suspensions. Still her feeling of trust towards her brother that had been getting stronger each day she spent with him. Her favor for him wouldn't disappear even knowing that he was up to something not so good. She eve found herself feeling even more drawn to him than before and the scariest part of it was that she didn't felt like this kind of pull had Something wrong with it. It felt good, she felt are and powerful when the two of them were alone.

She rolled over to see the clock on her nightstand. She had slept in and by this time her brother and Jace were surely gone and not coming back until afternoon. Clary went to see where were they now. She looked out the window in her room to see the beautiful view of Venice which was odd, on the three weeks that had been traveling they hadn't been on a place more than once and usually they would stay just one day. She was glad to be in Venice again since one afternoon wasn't enough to visit everything. Clary took her sketchbook and went downstairs determined in drawing the beautiful view.

 **A/N: Hey guys!!! Thank you a lot for reading and sorry for all the mistakes.**

 **LOVE Y'ALL**

 **-Zoe**


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